The Way It Is
by doodly-squat
Summary: After the fallout of Season two's finale, the Agent's of S.H.I.E.L.D. find themselves trying to continue on as best they can. SPOILERS for episodes 21 and 22 (S.O.S. parts 1 and 2)
1. Chapter 1

With growing dread, Fitz made his way down the hall. Today, he had to make it. He owed her that much.

 _Jemma…_

Once again that overwhelming flood of pain, regret and guilt seized him. It was too much. He slowed, allowing himself a long pause after each tentative step.

 _I'm so sorry, Jemma._

He was ashamed for putting this off, keeping himself busy with his research into the Kree Stone. After that first day, others had gathered the data for him. He hadn't been able to go into that room again, not after…

"Fitz?"

He turned and found Skye standing in the hall behind him. Swallowing hard, he tried to force out some explanation, but nothing came to him.

"It's okay." She walked up beside him, gently placing a hand on his shoulder. "I know."

"I-I just…" He stared back down the hall. The door was in view. "It's just...I-I…"

"You're not ready."

He looked back at Skye. She wasn't asking. There was no room for argument. She was telling him. Already, after only three months of commanding the few other inhumans who'd joined S.H.I.E.L.D., she'd developed that same calm, authoritative voice Coulson had mastered.

Somehow she'd pivoted Fitz around without him realizing it, and she was slowly leading him down the hall, away from his original destination.

A part of him wanted to pull away, to run to the room, to…

The memories from that day flooded back. Facing _that_ again terrified him, made him feel weak and useless. Nothing had changed. He'd failed her time and time again. Whatever pain she was in was his fault.

 _I'm so sorry, Jemma…_

* * *

Skye had watched Fitz from a distance. She knew where he was heading and that he'd never to able to make it. They'd all found him, at some point or other, standing in that hallway. Until someone came and led him away, he'd stand there, staring, grieving. She'd made it a habit to walk the hallway whenever she could, just to check.

Like the numerous times before, she'd take him back to his bunk, but he wouldn't stay, not for long. He'd wander back to his lab and resume his research on the Stone. He hardly ate. He barely slept, and it was becoming harder to get him to have any real form of conversation.

They made it to his room, and, to her surprise, he actually crawled onto his bed and lay down.

"Do you need anything? The mess hall is still open."

Eyes closed, he shook his head.

Skye waited, hoping for something more, even though she knew it wouldn't come. She studied him a moment, noting how pale he looked, how dark the bags were under his eyes. As much as she hated to do it, she'd contact the sickbay and ask someone to check in on him. Maybe Coulson could up the amount of sessions Fitz was having with DR. Garner.

"Tomorrow I'll stop by and we can have lunch," she added softly. It would be hard to make that promise fit into her schedule, but she'd do it.

He gave a tiny grimace and turned away. She couldn't blame him, not after all he'd faced.

She quietly left. There was nothing more she could do for him right now. He needed time, and she was late to her training class. She sighed. It was probably in bad form for the instructor to be late, but it was probably in worse form to have an instructor who still didn't know what the heck they were doing.

* * *

Hunter plastered on his best smile. This was, after all, paradise. Sandy beaches, tropical weather, beautiful sunsets, Bobbi had chosen well. They had everything they could ever need. There was no reason to leave, and they wouldn't, not ever again. His smile faltered a bit with that thought. Luckily, Bobbi didn't notice. She was too busy looking gorgeous, staring out at the sunset dappled ocean, breeze tousling her hair.

This was everything she wanted and everything he should have wanted, but…

He wasn't feeling it, not totally. Every Tuesday morning he'd get up before dawn and call Coulson. It was an arrangement they had and one Hunter was thankful for. This paradise was what Bobbi wanted, but he hadn't been ready, not yet. Perhaps if the news from Coulson had been better, if he didn't feel there was so much more he could still be doing.

Coulson's sources had discovered that Ward had revitalized Hydra. All attempts to stomp out the growing organization had failed so far. Because of Ward's familiarity with S.H.I.E.L.D., protocols all had to be rewritten and entirely new security measures installed.

Additionally, a new organization had formed from some of the agents who had been following Gonzales' old group. Gonzales' death had only strengthened their distrust of any alien influence, and they refused to join a S.H.I.E.L.D. organization that allowed inhumans to serve as agents. Apparently, this new group was calling themselves S.W.O.R.D. and their feelings on the inhumans and any alien artifact was to shoot first and ask questions never. Didn't they know that never ended well?

And finally, Simmons was still gone and Fitz was in a downward spiral. Even with all the danger and world destruction hanging over all the other issues Coulson spoke of, this was the one thing that hit Hunter the hardest. It was difficult to enjoy his paradise knowing that two good people, who probably deserved happiness more than him, were suffering.

"What are you thinking about?"

At the sound of her voice, he'd realized he'd let his façade drop, that the smile had melted away. He looked her straight in the eyes and grinned. "Nothing, Bobbi, just trying to decide if we should go to the feast tonight or stay in."

She smiled back, but he could see the tightness in it, the uncertainty. "Really? That's what you were thinking about?"

"Well, it's a very important matter to me. These things must be plotted out and weighed carefully. On one hand we have the most mouthwatering, delicious banquet a man could desire and on the other…" He raised a brow and scanned her bikini-clad body from head to toe.

She laughed. "So what did you decide?"

He leaned forward and nuzzled her cheek before whispering in her ear, "The same thing I always decide."

* * *

May frowned as she skimmed the report. Once again, Ward had managed to track down a S.H.I.E.L.D. safe house and annihilate it. Three agents were dead and two were missing, and she wasn't sure which was worse, dead or missing. Whatever Ward was doing to those missing agents couldn't be good.

Putting the tablet down, she stared blankly across the room, mentally assuring herself, once again, that she would be the one to end Ward.

No matter what her mixed feelings were about S.W.O.R.D. and the inhuman agents, she remained steadfast on what Ward's fate should be.

Killing Ward felt right. She missed the days when right and wrong felt more absolute, when she felt that she was on the side of good. Now, with powered people, alien artifacts, and mind control there were too many gray areas. Another Bahrain was looming on the horizon. She could feel it.

In fact, she already knew what her next Bahrain would be. May had been preparing herself for it for the past three weeks.

 _Simmons._

There would be no telling what kind of changes had taken place in Simmons, not until she was back. Then again, they might never get her back. May frowned. It was unbearable not knowing what had happened to Jemma, but having her back could potentially be worse.

That sinking feeling settled into May's stomach again. No one else would be able to do it, if it had to be done. Coulson would look to May. After all, she did it in Bahrain. This time though, she wasn't sure if she could heal from another mental wound that deep, and she wasn't sure the rest of the team would ever understand or forgive her for killing one of their own.

* * *

The coffee was cold, but he drank it anyway. Complaining was for people with time, and Coulson didn't have any of that. Fury practically had him running in three directions at once. A meeting in France, followed by negotiations in Canada with a few delegates from S.W.O.R.D., and all that ended with an operation in South America to root out one of Ward's new secret bases.

"How'd it all go?" Billy asked, sauntering into the room with a steaming cup of coffee that he quickly offered over.

"Better now," Coulson replied, taking in a whiff of the caffeinated goodness."Truthfully though?" He paused to take a sip. "It went terribly. The meeting in France was somewhat productive, but it also highlighted how far we are from setting any solid stances on the inhuman front. There are still a few naysayers in the bunch. Plus, the S.W.O.R.D. negotiations felt an awful lot more like the new kid in town was sizing me up to see how best to pummel me later. I'll have to remember to bring May with me next time."

"That would probably be for the best," Billy quipped.

"For me, yes, not for S.W.O.R.D."

"And the Operation in South America?"

Coulson frowned. "A complete disaster. If anyone from Hydra had been there, they cleared out long before we got there. All we managed to do was waste resources and scare the living daylights out of a bunch of poor farmers. I think we gave one of their cows a heart attack. And that operation was based on the most solid intel we've gotten in weeks."

"And Simmons?"

Coulson didn't bother to meet Billy's gaze, he just shook his head. That wasn't something he wanted to talk about, not if he didn't have to.

"That's too bad," Billy replied softly. "I'm sorry." For a moment the little man went silent. He only spoke again when Coulson glanced up. "Fury wants you to fly out again within the hour. It's a delicate matter. Some people in Kyowa, Japan have, um, died and others have turned. They need a team there immediately. Fury wants you to lead it."

 _Well, so much for a long, hot shower and a good meal._

Coulson nodded, "Okay, Billy, have the jet prepped and notify Skye and May. We roll in ten."

"Yessir!" Billy replied before hurrying out of the room in a flurry of lanyard-wrapped energy.

After one last sip of coffee, Coulson was up and on the move. May wouldn't be happy. She never was when he made her go on these missions, but she was one of the best agents he had. He couldn't afford to keep leaving her behind. Of course, she really wouldn't like going on a mission dealing with inhumans and working along side inhuman agents, but that couldn't be helped, not anymore. Eventually, she'd come around, he hoped.

* * *

Mack had the drones clear the area. In fact, he had them triple check the containment box to make sure no bolt was loose. Only then did he enter the room.

He hated going in. Every instinct he had told him to turn away, to seal the room off and never let anyone in there again. But, that was impossible.

Simmons was gone and it was his fault. Fitz might have prattled on about knocking a latch and leaving Simmons in a room by herself, but that wouldn't have been enough to let the Stone out. The containment box that housed the Kree Stone should have held through even Fitz's clumsy stumbles. It should have.

There was a design flaw, one Mack was responsible for. Coulson had put him in charge of the alien artifacts. He'd thought he'd been careful. He'd been sure of it, but the constant movement, that tidal wave flow of the Kree Rock had worked loose the screws on the containment latch. Why hadn't he thought to check those?

The Rock, as if sensing Mack was near, turned to liquid and pounded against the containment wall. Reforming, it stood, suddenly quiet and still again.

Mack stared a minute, waiting. Soon it would happen. It was best to deal with it quickly, to get it over with.

The voice was low, at first. He could hear the pain in it though. Goosebumps rose on his arms as he listened.

"Help me, please. I'm alone. Help me…I want out, please. It hurts!"

The shape formed then, emerging from the rock, but still as black and glossy as the stone itself. Slowly the features became defined and Simmons stood there in front of Mack.

 _No, not Simmons._

He had to remember that. He'd taken the readings. This thing had no life signs. It was only cold stone using her image. It wasn't her.

"You can just go on back into your rock home." He said, keeping eye contact with the thing the entire time. "I'm not falling for any of your tricks. You know me by now and you know I'm telling the truth."

The pleading stopped swiftly, and a fleeting moment of disdain and hatred flooded the familiar face. Then, the figure took two backwards steps and disappeared into the stone.

He looked for that every time, for that instant of pure animosity on the thing's face. That was how he really knew this wasn't Jemma. Unlike the others, Mack was sure Jemma was dead, or, at least for her sake, he hoped she was.

With the horrible ritual over with, he checked the containment box one last time and then started to set up his equipment to take the readings Fitz needed.

* * *

It was dark, but it was always dark, so that wasn't unusual. Sometimes her skin tingled though and sometimes her bones ached. Then there were the times she'd simply black out. At least she could keep track of the black outs with her stopwatch. She'd set it running the moment she'd remembered it in her pocket. In a world of darkness, it was nice to have some semblance of normalcy to cling to.

Jemma would estimate the time based off how long the stopwatch had been running. Then, she'd ponder over what the other agents were doing, or what she would have been doing had she been back home. Plus, when she returned, the comparison of elapsed time would be fascinating. She highly suspected that time inside the stone moved slower. She believed that the stone itself might work as some sort of almost suspended animation compartment.

Fortunately, she didn't seem to require substance or suffer from thirst while in the stone, and she kept herself occupied with a schedule of exercise, study and sleep. While the exercise and sleep aspects were not difficult, the study became more challenging, but it was not impossible. The important thing was not to panic and to stay focused.

They would come for her. She knew it. Fitz would get her out. There was no doubt in her mind. After all, according to her stopwatch, it had only been three days.


	2. Chapter 2

"None of this makes any sense!" Fitz tossed his tablet aside. Cupping his hands over his face, he rubbed his forehead, trying desperately to ease the tension building beneath his skull.

 _If Jemma were here, she'd know what to do. She'd know how to solve this._

"Hey now," Mack called out. "No need for that."

Fitz raised his head and scowled at the big man. He'd forgotten the blasted Mech was in the room. The man could be quieter than a damn mouse. It was great sharing a work space with him, but it was frustrating forgetting someone was in the room, especially when Fitz was trying to hold a perfectly good solo self-belittlement conversation.

Mack put down the engine part he'd been greasing and made his way over to Fitz. "What seems to be the problem, Speedy?"

 _Great, now I get to go over my failures all over again._

Fitz sighed and snatched his tablet back up. He held it up for Mack to see as he swiped through pages of data. "None of this makes sense. It's all…There's…It's just…"

"Hold up. Just give yourself a minute to think it through, and then tell me again. What is wrong with the data?"

Fighting the urge to hurl the tablet across the room, Fitz took a deep breath and closed his eyes. What was wrong with the data? What…was…wrong…with…

"It's all the same," Fitz answered softly. "The deviations aren't enough to give any indication that this thing is anything more than a stupid rock. It should…There should…"

Mack raised a brow. "Be more?"

"YES!" Fitz snapped. "There should be loads more. It should read more like this little blurb here." He scrolled back three pages and pointed to one sharp spike at the start of a string of data. "But there's nothing else like that in the readings you brought me. For months, there's been nothing like that."

"You need that?" Mack's tone went cold, flat. "You sure?"

"Yeah. Yeah, I'm sure. I need _that."_ He jabbed at the tablet again. "I need that—more of that. Can you get it?" For the first time in weeks, Fitz felt a pang of hope.

"I can, I think."

The fact that Mack was not reveling in this potential breakthrough immediately had Fitz on edge. There was something the big man wasn't telling him.

"What?" Fitz pressed. "What is it?"

"Nothing."

 _He doesn't think I'm really letting it go that easily, does he?_

Gently setting down his tablet, Fitz crossed his arms and positioned himself squarely in front of the Mech. "Let me be the judge of whether it's nothing or not. Spill."

Mack shrugged and started to turn away. "Seriously, it's nothing."

"TELL ME!" Fitz surprised even himself with the ferocity that came out with.

For a good couple of minutes, they both stood silently in place, and then, just as Fitz thought he'd get no answer, Mack slowly turned back around. A weary sadness had etched its way onto the big man's face.

"That data spike," Mack replied, "only happens when it looks like her." He grimaced. "And, that thing disappears when I get the equipment up and running. Plus, I'm not exactly its favorite person anymore. It doesn't hang around much at all now."

In seconds, Fitz was bathed in a cold sweat. He tried to hide the fact that his breath was becoming a little too labored, that his heart was racing so fast he thought he might pass out.

"Can you set up the equipment? Just let it run?" he asked.

Mack nodded. "Yeah, but it won't do any good. It won't come out."

"Yeah," Fitz muttered, "it will. It will if I go back into the room."

Mack's argument started up quickly, but it didn't matter. In fact, Fitz was hardly listening. Whatever Mack had to say would make no difference. This was happening. There was no way around it. There would be no excuses. This time, Fitz wasn't going to fail Jemma.


	3. Chapter 3

No matter how many times he'd tried to mentally prepare himself, or how many times he'd already witnessed the tragedy firsthand, Coulson was never ready. This time was no different.

Twenty-three lives had ended. In the grand scheme of things, some would argue that the number really wasn't high. That, Coulson knew, was not only an apathetic stance, it was a foolish one as well.

Twenty-three had died, but hundreds would grieve, and entire populations would cultivate fear, prejudice and, eventually, hate.

He stared out the Quinjet's window, catching glimpses of starlight through the banks of clouds.

His thoughts wandered back to Japan, to the mother frantically searching for a boy she'd never find, to the children pleading for the S.H.I.E.L.D. agents to find their father, and to the old man, frail and thin, who wept so fiercely for the loss of his wife. From memory, Coulson methodically ran through the list, until he'd reached the twenty-third victim; the beggar, whose passing almost went unnoticed.

"I might never eat sushi again."

Looking up, he flashed Skye a weak smile as she sat down next to him.

"Hard to believe what one contaminated batch of fish can do, isn't it?" He replied. "And it was hit and miss on which fish was tainted and which wasn't. All from the same part of the ocean and only a fraction contained the Mist compound."

"It was lucky for the village that all the fish weren't contaminated. That would've wiped them out. Well, nearly wiped them out." Skye glanced back at the two figures dozing in their seats near the rear of the jet.

"How are they doing?" He asked, though he had a good notion of what the answer would be.

She shook her head. "Too early to tell."

" _But_?"

Skye tilted her head and narrowed her eyes at him. "But, _what_?"

"It might just be my imagination, but I'd swear I've seen a certain amount of unease cross your face more than once as you handled those two."

"They're two brand-spanking-new inhumans with unstable powers," she deadpanned. "A certain amount of unease is expected."

"For some people, maybe, but not from you and not like that." It was a hard truth, but part of his job was pointing out the hard truths.

He expected the silence. Skye had to gather her thoughts. She was careful whenever discussing inhumans. She knew all too well what it felt like to be unfairly branded as something dangerous or monstrous.

"The girl, Kasumi," she said, at last. "There is something about her, about the fascination she has with her power. I think, someday…" Skye trailed off, gaze wandering to the back of the Quinjet again. "…she's going to hurt people."

 _That_ Coulson hadn't expected. He'd suspected the twelve-year-old, Kasumi, was going to be a handful. After all, the kid was a human microwave. He'd watch her pop a bag of popcorn just from holding it in her hands. Still, she seemed shy, reserved and, oddly, almost totally in control of her powers.

If Skye had her suspicions though, Coulson wasn't about to take them lightly. "What makes you think that?"

"Before we left," Skye answered quietly, "I found her all alone, outside by the creek. She had a bunny, and she was petting it so sweetly. There was a moment when I didn't realize what was happening, before the heat reached the surface." Skye met Coulson's gaze. "She'd burned it from the inside out, and then she looked up at me, smiled and said ' _I did that.'_ She was proud of it. She was… _delighted."_

 _Yeah, that could definitely be a problem._

"And you waited to tell me this until we were confined in a jet 10,000 feet in the air?"

Skye shrugged. "Not my best move ever, I'll admit, but where would she be if I had told you?"

Okay, she had him on that one. Coulson had to give her that.

"Right where she's at now, I guess." He declined to mention that he probably would've considered carrying an I.C.E.R. though. Skye's powers would probably be sufficient enough to knock out one twelve-year-old kid, if the need arose.

"Besides," she added, "Masato seems to balance her, to keep her calm."

Coulson smiled. The short, plump, bumbling Masato was hardly what he'd expected to find. Even the man's gift was, to say the least, different. As far as they could gather, Masato could slightly raise or lower the temperature in a fairly small, well defined area. Truthfully, if Masato hadn't also grown transparent third eyelids, Coulson probably wouldn't have pegged the man as an inhuman.

What Masato seemed to lack in powers, he made up for in sheer exuberance. He'd already begged Coulson to take him on as a S.H.I.E.L.D. agent. The Avenger trading cards Masato eventually scrounged out of his room while he was packing up his belongings only fueled his determination.

" _I will be an Avenger someday,"_ he'd told Coulson, all while smiling happily, staring at his cards, and, occasionally, blinking those reptilian eyelids. " _I will make things a little warmer and a little cooler and I will save the world!"_ He'd chuckled after that, saying that perhaps being an Avenger was too much, but he added, quite earnestly, that he pledged to be a _very_ good agent.

"Masato is an asset." Coulson replied. "His powers might surprise us, someday."

Skye remained silent, her gaze set on Masato and Kasumi. Jaw clenched, body tense, if Coulson didn't know better, he'd have sworn she was on guard, waiting for…

Suddenly, the Quinjet quivered and then violently began to drop.


End file.
